Description Usage Arguments Details Author(s) See Also Examples
This function creates plots for one or more of the 'B AlleleFreq', 'Log R Ratio', 'R' or 'Theta' values for given sample by chromosome combinations.
1 2 3 4 5 6 7 8 9 10 | chromIntensityPlot(intenData, scan.ids, chrom.ids,
type = c("BAF/LRR", "BAF", "LRR", "R", "Theta", "R/Theta"),
main = NULL, info = NULL, abln = NULL,
horizln = c(1/2, 1/3, 2/3),
colorGenotypes = FALSE, genoData = NULL,
colorBatch = FALSE, batch.column = NULL,
snp.exclude = NULL,
ideogram=TRUE, ideo.zoom=TRUE, ideo.rect=FALSE,
cex=0.5, cex.leg=1.5,
colors = c("default", "neon", "primary"), ...)
|
intenData |
|
scan.ids |
A vector containing the scan IDs to plot. |
chrom.ids |
A vector containing the chromosomes to plot for each
scanID (should have same length as |
type |
The type of plot to be created. 'BAF/LRR' creates both 'B Allele Freq' and 'Log R Ratio' plots. 'R/Theta' creates both 'R' and 'Theta' plots. |
main |
Vector of plot titles. If |
info |
A character vector containing extra information to include in the main title. |
abln |
A vector of values that is of length |
horizln |
A vector containing the y-axis values at which a horizontal line will be drawn in B Allele Frequency plots. |
colorGenotypes |
A logical value specifying whether to color-code
the points by called genotype. if |
genoData |
|
colorBatch |
A logical value specifying whether to color-code the
points by sample batch (e.g, plate). If |
batch.column |
A character string indicating which annotation variable in intenData should be used as the batch. |
snp.exclude |
An integer vector giving the IDs of SNPs to exclude from the plot. |
ideogram |
logical for whether to plot a chromosome ideogram under the BAF and LRR plots. |
ideo.zoom |
logical for whether to zoom in on the ideogram to match the range of the BAF/LRR plots. |
ideo.rect |
logical for whether to draw a rectangle on the ideogram indicating the range of the BAF/LRR plots. |
cex |
cex value for points on the plots. |
cex.leg |
cex value for the ideogram legend. |
colors |
Color scheme to use for genotypes. "default" is colorblind safe (colorbrewer Set2), "neon" is bright orange/green/fuschia, and "primary" is red/green/blue. |
... |
Other parameters to be passed directly to |
For all plots, a vertical line is drawn every one eigth of the chromosome. For the Log R Ratio plot, the y-axis has been given the range of (-2,2).
Caitlin McHugh, Cathy Laurie
IntensityData
, GenotypeData
,
BAFfromGenotypes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | library(GWASdata)
data(illuminaScanADF)
blfile <- system.file("extdata", "illumina_bl.gds", package="GWASdata")
bl <- GdsIntensityReader(blfile)
intenData <- IntensityData(bl, scanAnnot=illuminaScanADF)
genofile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
geno <- GdsGenotypeReader(genofile)
genoData <- GenotypeData(geno, scanAnnot=illuminaScanADF)
scanID <- getScanID(illuminaScanADF, index=1)
chromIntensityPlot(intenData=intenData, scan.ids=scanID,
chrom.ids=22, type="BAF/LRR", info="interesting sample",
colorGenotypes=TRUE, genoData=genoData)
close(genoData)
close(intenData)
|
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